content stringlengths 35 762k | sha1 stringlengths 40 40 | id int64 0 3.66M |
|---|---|---|
import logging
def find_bad_positions(coverage_matrix, target_folder = None, trait = None, samplename = None,
trait_cutoff = None, whitelist = None):
"""
Walk through all bases and find contigous regions of bases that fail the coverage/strandbias cutoff
Create an output fil... | 02fbcb688fc763a414805c3c898027c14b12b9f0 | 35,500 |
def s_norm(p_string, uppercase=False):
"""
Filters out all punctuation, normalizes the casing to either
lowercase or uppercase of all letters, and removes extraneous
whitespace between characters. That is, all whitespace will
be replaced by a single space character separating the words.
:param p_string
The str... | 69519ddfb2fd58bab3b6db9695946a168ce3eec4 | 35,501 |
def _venv_changed(session: nox.sessions.Session) -> bool:
"""Return True if the installed session is different to that specified in the lockfile."""
result = False
if _venv_populated(session):
expected = _file_content(_session_lockfile(session))
actual = _file_content(_session_cachefile(sess... | a5723d9e3f5f71f3f7b83dc0bfa6ed659c9dca13 | 35,502 |
import random
def greedy_policy(A, s, Q, epsilon = None):
"""在给定一个状态下，从行为空间A中选择一个行为a，使得Q(s,a) = max(Q(s,))
考虑到多个行为价值相同的情况
"""
max_q, a_max_q = -float('inf'), []
for a_opt in A:
q = get_dict(Q, s, a_opt)
if q > max_q:
max_q = q
a_max_q = [a_opt]
elif ... | 12ae83e3c28e6d65d4b3cc81aa712657c82834c3 | 35,503 |
def login_user(cursor, username):
""" create new session for user with username, return session key """
userid = get_userid(cursor, username)
key = token_urlsafe()
cursor.execute(
"REPLACE INTO sessions ('userid', 'key') VALUES (?, ?)",
(userid, key)
)
return key | b507aa966608a372df785b3e7d3c8a1a26c2d23a | 35,504 |
def tapisize(fieldKeyName):
"""Transforms a string into a Tapis query parameter
"""
return fieldKeyName.lower() | cc8032a6cc9e822193430134bb33da8aef74cf06 | 35,505 |
def get_minions(returner):
"""
Return a list of all minions
CLI Example:
.. code-block:: bash
salt '*' ret.get_minions mysql
"""
returners = salt.loader.returners(__opts__, __salt__)
return returners["{0}.get_minions".format(returner)]() | f4dd2a96884ddfc356b3214b89bfd1da96e15a40 | 35,506 |
from typing import Union
import torch
def nx_second_order_proximity(
G: Union[nx.Graph, nx.DiGraph],
node_ids: Union[Tensor, ndarray, list],
whole_graph_proximity: bool = True,
to_batch: bool = False,
distance_metric: str = "cosine",
norm_rows_in_sample: bool = False,
norm_rows: bool = Tru... | 1eb2e37e0d52b0428843f71adc901a02c62eadb5 | 35,507 |
def calculate_average_resolution(sizes):
"""Returns the average dimensions for a list of resolution tuples."""
count = len(sizes)
horizontal = sum([x[0] for x in sizes]) / count
vertical = sum([x[1] for x in sizes]) / count
return (horizontal, vertical) | 06dac1834989df96ce7bff88c435dd4067bfccbd | 35,508 |
def is_enum0(*args):
"""
is_enum0(F) -> bool
Is the first operand a symbolic constant (enum member)?
@param F (C++: flags_t)
"""
return _ida_bytes.is_enum0(*args) | 137b34efa475738ff3a9d1633822f1a1c7a0ca32 | 35,509 |
def view(image, ui_collapsed=False, annotations=True, interpolation=True,
cmap=cm.viridis, mode='v', shadow=True, slicing_planes=False, gradient_opacity=0.2):
"""View the image.
Creates and returns an ipywidget to visualize the image.
The image can be 2D or 3D.
The type of the image can be an... | 5c71f27ba46258ad97dade0cab04fbf65e8e3c22 | 35,510 |
import click
def install_chute(ctx, chute, node, follow, version):
"""
Install a chute from the store.
CHUTE must be the name of a chute in the store. NODE must be the
name of a node that you control.
"""
client = ControllerClient()
result = client.install_chute(chute, node, select_versio... | 90781fc0c9d4cca877f44b9b93be2c8d075fa4a3 | 35,511 |
from pathlib import Path
def create_folder(subfolder: str,
folder: str) -> None:
"""
Function for creating folder structure for saved stationdata
"""
path_to_create = Path(folder, subfolder)
Path(path_to_create).mkdir(parents=True, exist_ok=True)
return None | e50052d22cb8385e1c3a83caa643ec0d0289d1b0 | 35,512 |
import sys
import os
def source_provider_blender(filename):
"""
Return source code of the file referred by filename.
Support for debugging of Blender Python scripts.
Blender scripts are not always saved on disk, and their
source has to be queried directly from the Blender API.
http://www... | beec37ecb12d487beff12488898757a26e6bb223 | 35,513 |
def locate_spikes_peakutils(
data, fps=58.21, thresh=0.7, min_dist=None, max_allowed_firing_rate=1
) -> np.ndarray:
"""
Find spikes from a dF/F matrix using the peakutils package.
The fps parameter is used to calculate the minimum allowed distance \
between consecutive spikes, and to disqualify cell... | e32c8ebc8024b4547592769744051b6d30897851 | 35,514 |
def has_valuable(camera):
"""Function checks if the camera sees any valuable.
@param camera: webots camera object to use for the recognition
@returns True if a valuable is detected, False otherwise
"""
# Check if camera has recogniton and is enabled
if not camera.hasRecognition() or camera.getRe... | 5ff65e4dc52abbcd42700168fb7aa26e83aa2aab | 35,515 |
def _partition_fold(v,data):
"""
partition the data ready for cross validation
Inputs:
v: (int) cross validation parameter, number of cross folds
data: (np.array) training data
Outputs:
list of partitioned indicies
"""
partition = []
for i in range(v):
if i... | fc833b5120c5d8e479af1758f86e0541c5d7d87c | 35,516 |
def get_distance(m, M, Av=0):
"""
calculate distance [in pc] from extinction-corrected magnitude
using the equation: d=10**((m-M+5-Av)/5)
Note: m-M=5*log10(d)-5+Av
see http://astronomy.swin.edu.au/cosmos/I/Interstellar+Reddening
Parameters
---------
m : apparent magnitude
M : absol... | b4773065d7cf1bc793400ac344c4ca7a580f8567 | 35,517 |
def get_csr_as_text(csr_filename):
"""Convert CSR file to plaintext with OpenSSL."""
return _run_openssl(['req', '-in', csr_filename, '-noout', '-text']).decode('utf-8') | f08d1d914b992474e2c51406bab58f2f2ad37c6c | 35,518 |
from typing import List
from pydantic import BaseModel # noqa: E0611
def search_filter_sort_paginate(
db_session,
model,
query_str: str = None,
filter_spec: List[dict] = None,
page: int = 1,
items_per_page: int = 5,
sort_by: List[str] = None,
descending: List[bool] = None,
current... | 60f1b769a5ccafeeb6da01412f439a4f1234e75f | 35,519 |
def rename_entry(*args):
"""
rename_entry(ord, name, flags=0x0) -> bool
Rename entry point.
@param ord: ordinal number of the entry point (C++: uval_t)
@param name: name of entry point. If the specified location already
has a name, the old name will be appended to a repeatable
... | d70cd7b42b8e6b4e748c7c2599a46859dd5f6059 | 35,520 |
from typing import Iterable
from typing import Tuple
def split_file_to_annotations_and_definitions(lines: Iterable[str]) -> Tuple[EnumLines, EnumLines, EnumLines]:
"""Enumerate a line iterable and splits into 3 parts."""
enum_lines = sanitize_file_lines(lines)
metadata, definitions, statements = multi_spl... | 64a5f6f4d32f80d90f1247472564ae04e902ae1d | 35,521 |
def _SafeCreateLogoutURL(mr):
"""Make a logout URL w/ a detailed continue URL, otherwise use a short one."""
try:
return users.create_logout_url(mr.current_page_url)
except users.RedirectTooLongError:
if mr.project_name:
return users.create_logout_url('/p/%s' % mr.project_name)
else:
retur... | 06ee47ba38abb660096bace71704ddd0becd465a | 35,522 |
from typing import Tuple
from typing import Dict
def random_speech_to_text(
draw
) -> st.SearchStrategy[Tuple[SpeechToTextGen, Dict]]:
"""Generates different speech_to_text functions."""
kwargs = draw(random_speech_to_text_kwargs())
return speech_to_text(**kwargs), kwargs | 035d905aba274f1083daae07e2492f9ae84cd21f | 35,523 |
def line_neighbor_score(mat, idx, line_width=1, distance_range=(20, 40), window_size=5,
line_trick='min', neighbor_trick='mean', metric='diff'):
"""
:math: enrichment-score = line-trick(line) - neighbor-trick(neighbor)
:param idx: (int) stripe location index
:param mat: (2D ndar... | a3b4a49479c5bcf7f12e4bb23affda942ec3670e | 35,524 |
def plugin_name_to_layerapi2_label(plugin_name):
"""Get a layerapi2 label from a plugin name.
Args:
plugin_name (string): the plugin name from which we create the label.
Returns:
(string): the layerapi2 label.
"""
return "plugin_%s@%s" % (plugin_name, MFMODULE_LOWERCASE) | c91a5c463e3b15e324c049e9557a2711031dcb95 | 35,525 |
def unscii(font_name):
"""
Given a font name, return a font object for usage.
"""
return UnsciiFont(font_name) | 41a8a03417d1d231cbd2bf99b09d8efd98afcd8c | 35,526 |
def get_environ_dict():
"""Return a dictionary of all environment keys/values."""
return {
'os.environ': _get_os_environ_dict((
'AUTH_DOMAIN',
'CURRENT_CONFIGURATION_VERSION',
'CURRENT_MODULE_ID',
'CURRENT_VERSION_ID',
'DEFAULT_VERSION_HOSTNAME',
'FE... | 056b8499db4dbc14db904eb5f1c01ed49ae39a18 | 35,527 |
def k_from_a_ea(a, e_a, temp, r_gas):
"""
convert using "alternate" form of Arrhenius eq
:param a: pre-exponential factor
:param e_a: activation energy with units consistent with given r_gas
:param temp: temperature in K
:param r_gas: universal gas constant in units consistent with e_a and temps... | 79415b8ee583e03282d7ab02b5e255d611e5677f | 35,528 |
import argparse
def get_args_parser(PORT: int = 4500):
"""
Extendable parser for input arguments
Args:
PORT: default port to be exposed
"""
parser = argparse.ArgumentParser(add_help=True,
description="Backend service API")
parser.add_argum... | 8fcddec4df5f64c9425a028432ad7c80eae6542f | 35,529 |
def extract_source_info(df_adverse_ev):
""" Find information about who submitted the report """
qual_list = []
for i in range(0,len(df_adverse_ev)):
if df_adverse_ev.iloc[i]['primarysource'] is not None:
col_names = list(df_adverse_ev.iloc[i]['primarysource'].keys())
if 'qual... | 246571a57467b03ed5f5bd2456108e4b93ec136f | 35,530 |
import json
def load_base_models_json(filename="base_models.json"):
"""Load base models json to allow selecting pre-trained model.
Args:
filename (str) - filename for the json file with pre-trained models
Returns:
base_models - python dict version of JSON key-value pairs
"""
with... | c17f123e192b94e6f87938bca10822ea785e2d91 | 35,531 |
def _parsedatetime_parse(date_string):
"""Parse the given date_string using the parsedatetime module."""
# for more details on how the parsedatetime.Calendar.parse function works, see:
# https://github.com/bear/parsedatetime/blob/830775dc5e36395622b41f12317f5e10c303d3a2/parsedatetime/__init__.py#L1779
c... | a8ce67294d9c035c0777a2d1c0a4fe6e43f65154 | 35,532 |
import sys
import os
def main(argv=None, directory=None):
"""
Main entry point for the tool, used by setup.py
Returns a value that can be passed into exit() specifying
the exit code.
1 is an error
0 is successful run
"""
argv = argv or sys.argv
# Init the path tool to work with the... | b7b0f1930d9631d1c99ca1cb045f98d1589d6f1a | 35,533 |
from pathlib import Path
import sys
def read_tsv_or_parquet(filepath):
"""Read either a TSV or a parquet file by file extension."""
filepath = Path(filepath)
if not filepath.exists():
logger.error(f'File "{filepath}" does not exist.')
sys.exit(1)
ext = filepath.suffix.lstrip(".")
i... | 6cbe14ec9a110d34220e2bbb1eaf9ffe194646cd | 35,534 |
def BFMM(
source,
target = None,
charge = None,
dipole1 = None,
dipole2 = None,
compute_source_velocity = False,
compute_source_analytic_gradient = False,
compute_source_anti_analytic_gradient = False,
compute_target_velocity =... | e1fbce824777c1d260e1e83a8a8fe7b1b2d05886 | 35,535 |
import sys
def blast(args):
"""
%prog blast fastafile
Run BLASTN against database (default is UniVec_Core). Output .bed format
on the vector/contaminant ranges.
"""
p = OptionParser(blast.__doc__)
p.add_option(
"--dist",
default=100,
type="int",
help="Merg... | 15c5e5096079be9b10ac07a4f82ede511727fc05 | 35,536 |
def get_dihedrals(a, b, c, d):
"""
A function that gets dihedral angles between two residues.
See set_neighbors6D for usage.
"""
b0 = -1.0*(b - a)
b1 = c - b
b2 = d - c
b1 /= np.linalg.norm(b1, axis=-1)[:,None]
v = b0 - np.sum(b0*b1, axis=-1)[:,None]*b1
w = b2 - np.sum(b2*b1, ... | 91897e67e7d73eeb60dc73b2ba45e1aaeec5c470 | 35,537 |
def iexact(self, compiler, connection):
"""A method to extend Django IExact class. Case-insensitive exact match.
If the value provided for comparison is None, it will be interpreted as
an SQL NULL.
:type self: :class:`~django.db.models.lookups.IExact`
:param self: the instance of the class that own... | ebe51c6b8c34a0cc1746169e8fe6e8eb79e01152 | 35,538 |
import json
def load_data_from_json(jsonfile):
"""Load the data contained in a .json file and return the corresponding Python object.
:param jsonfile: The path to the .json file
:type jsonfile: str
:rtype: list or dict
"""
jsondata = open(jsonfile).read()
data = json.loads(jsondata)
r... | f0f7a0620be8ffcd15a57fd561dda8525866faa3 | 35,539 |
def grpc_check(fpath):
"""
Check whether grpc service is enabled in this .proto file.
Note: only proto file with the following form will pass our check.
service MyService {
rpc MethodA(XXX) returns (XXX) {
rpc MethodB(XXX)
returns (XXX) {
}
}
"""
if not f... | 17a1539f8913bb35d2e89f31d7f48acbc1f35b54 | 35,540 |
def bb_intersection_over_union(boxA, boxB):
"""
Computes IoU (Intersection over Union for 2 given bounding boxes)
Args:
boxA (list): A list of 4 elements holding bounding box coordinates (x1, y1, x2, y2)
boxB (list): A list of 4 elements holding bounding box coordinates (x1,... | 290d625dd3ed7ab37ecf3aa7f39a3b1727cecec0 | 35,541 |
import os
def apath(path='', r=None):
"""Builds a path inside an application folder
Args:
path(str): path within the application folder
r: the global request object
"""
opath = up(r.folder)
while path[:3] == '../':
(opath, path) = (up(opath), path[3:])
return os.path... | 3d3e4c7db037281a93b929135ac180110d45bc1b | 35,542 |
def area(boxlist, axis=-1):
"""Computes area of boxes.
Args:
boxlist: BoxList holding N boxes
scope: name scope.
Returns:
a tensor with shape [N] representing box areas.
"""
with tf.name_scope('Area'):
x_min, y_min, x_max, y_max = tf.split(value=boxlist, num_or_... | 6c0e791b021d5196651c0b1830019f23840596fd | 35,543 |
def _MatrixTriangularSolveGrad(op, grad):
"""Gradient for MatrixTriangularSolve."""
a = op.inputs[0]
adjoint_a = op.get_attr("adjoint")
lower_a = op.get_attr("lower")
c = op.outputs[0]
grad_b = linalg_ops.matrix_triangular_solve(
a, grad, lower=lower_a, adjoint=not adjoint_a)
if adjoint_a:
grad_... | 3faac87370dd9dfa589174976c7dd6bed76e4628 | 35,544 |
from typing import Dict
from typing import Any
def list_persons_command(client: Client, args: Dict[str, Any]) -> CommandResults:
"""Get persons list from TOPdesk.
Args:
client: The client to preform command on.
args: The arguments of the persons command.
Return CommadResults of list of p... | 8fb8c1065b433e7821fa46d64332c2238d502f7f | 35,545 |
def group_user_delete(user, group):
"""Delete an user from a certain group"""
if not pagure_config.get("ENABLE_USER_MNGT", True):
flask.abort(404)
if not pagure_config.get("ENABLE_GROUP_MNGT", False):
flask.abort(404)
form = pagure.forms.ConfirmationForm()
if form.validate_on_submi... | bc813bb31aed7798a59b117f7e1fb984f96dfc3b | 35,546 |
def repair_follow_organization_view(request):
"""
Process the new or edit organization forms
:param request:
:return:
"""
# admin, analytics_admin, partner_organization, political_data_manager, political_data_viewer, verified_volunteer
authority_required = {'verified_volunteer'}
if not v... | 38a78fdc21ab6c9b0a06e8447462fe5580e3df1c | 35,547 |
def vect3_add(v1, v2):
"""
Adds two 3d vectors.
v1, v2 (3-tuple): 3d vectors
return (3-tuple): 3d vector
"""
return (v1[0]+v2[0], v1[1]+v2[1], v1[2]+v2[2]) | b43fde71f0cc5e927879a2b6942c60de8ac6cc79 | 35,548 |
def voucher_received(cadde_provider=None, cadde_consumer=None, cadde_contract_id=None, hash_get_data=None, contract_management_service_url=None): # noqa: E501
"""API. データ証憑通知（受信）
来歴管理I/Fにデータ証憑通知（受信）を依頼する。
Response:
* 処理が成功した場合は200を返す
* 処理に失敗した場合は、2xx以外を返す。Responsesセクション参照。 # noqa: E501
:... | 28b4e29ea2d152a7c6f21581d3832ee77262fb0a | 35,549 |
import multiprocessing
def get_task_pool(thread=False):
"""
Get a new task pool, which is either a single-thread or process pool depending on the current config.
Returns:
A new :class:`multiprocessing.pool.Pool` instance.
"""
if thread or not config['app_multicore'] or config['enable_bac... | 515ae5c2ac167df1eb0f4ba2c3d4795a9830e3eb | 35,550 |
def get_date(article: ElementTree) -> int:
"""
Extracts the year of the article. If ArticleDate exist use its year
otherwise use the year form JournalIssue
"""
d = article.find("ArticleDate")
if d is not None:
return int(d.find("Year").text)
d = article.find("Journal").find("JournalI... | 3ca2f13d234df411e904195d9d1c08534ada1cea | 35,551 |
def split(column, pattern=''):
"""
Splits str around pattern (pattern is a regular expression)
> pattern is a string representation of the regular expression
"""
return _with_expr(exprs.StringSplit, column, pattern) | d091a5e89adf0d5de994b9a11c1c856cea5a8494 | 35,552 |
import gc
def convert(
model,
source="auto",
inputs=None,
outputs=None,
classifier_config=None,
minimum_deployment_target=None,
convert_to='nn_proto',
**kwargs
):
"""
Convert TensorFlow or Pytorch models to the Core ML model format. Whether a
parameter is required may diffe... | 0de2d8cb9ba2926b05262ea1754b112845b65033 | 35,553 |
def precut(layers, links, all_terms, user_info):
"""
This function cuts terms in layers if they do not exist inside
the accuracy file of model 1.
It also cuts all links if one of the terms inside does not exist
inside the accuracy file of model 1.
Finaly it cuts all terms taht do not exist insid... | cf04eec77d01ad931f7654a3743baaf51aad53fa | 35,554 |
def computeMeanStd_binned_old( inDatas, valCol, binCol, binMin, binMax, binCount ):
"""Compute binned stats for a set of tables"""
sums = np.zeros( binCount )
sumsSq = np.zeros_like( sums )
counts = np.zeros_like( sums )
bins = np.linspace( binMin, binMax, binCount+1 )
binSize = ( binMax - binMin ) / binCo... | 195fc421b3091725e629e05e27c64a862c7fc31b | 35,555 |
def Compute7(surface, multiple=False):
"""
Computes an AreaMassProperties for a surface.
Args:
surface (Surface): Surface to measure.
Returns:
AreaMassProperties: The AreaMassProperties for the given Surface or None on failure.
"""
url = "rhino/geometry/areamassproperties/compu... | f844f43b372ac2c8f124c27e346f9805583c3240 | 35,556 |
from typing import Optional
from typing import Union
def instantiate(config: Optional[Union[str, ClassDescription]], *args, **extra_kwargs):
"""Instantiates class given by `config.cls` with
optional args given by `config.args`
"""
try:
if config is None:
return None
elif ty... | c0f8f951212bb157b4ee8805615f83bad82db8e2 | 35,557 |
async def get_hm_generic_entity(
central_unit: CentralUnit, address: str, parameter: str
) -> GenericEntity | None:
"""Return the hm generic_entity."""
hm_device = get_hm_device(central_unit, address)
assert hm_device
hm_entity = hm_device.entities.get((address, parameter))
assert hm_entity
... | 25f2845951d7ab34155b7ee2347a8438b115a1eb | 35,558 |
def dists2corners_numpy(a):
"""
:param a: dist ndarray, shape = (*, h, w, 4=(t, r, b, l))
:return a: Box ndarray, shape is (*, h, w, 4=(xmin, ymin, xmax, ymax))
"""
assert a.ndim >= 3, 'must be greater than 3d'
h, w, _ = a.shape[-3:]
# shape = (*, h, w, 4=(xmin, ymin, xmax, ymax))
ret =... | 3f20df4cb3bc8ab1f1a595e64514e7b722fd07a1 | 35,559 |
def cryptowatch_ohlc_data_for_pair(Pair):
"""gets ohlc data from cryptowatch, and return a dict of dataframes"""
exchanges = list(Pair.markets)
data = {}
for ex in exchanges:
data[ex] = cryptowatch_ohlc(Pair.name, ex, Pair.period, Pair.start, Pair.end)
return data | 4f482ae1575d68e193321db0c2bd7346d4bf0950 | 35,560 |
from io import StringIO
def to_string_stream(x):
"""
For modules that require a encoding as ``str`` in both Python 2 and
Python 3, we can't just encode automatically.
"""
if PY2 and isinstance(x, text_type):
x = x.encode('utf-8')
return StringIO(x) | 8fd36bab988410881a560d27d4e8d54d36f58634 | 35,561 |
import os
def get_all_scores(pdb_path, reference_pdb_path):
"""Assigns scores (lrmsd, irmsd, fnat, dockQ, bin_class, capri_class) to a protein graph
Args:
pdb_path (path): path to the scored pdb structure
reference_pdb_path (path): path to the reference structure required to compute the diffe... | 7900a6f26d633aef7a12cd382f1be7dbcfeec2fc | 35,562 |
def run_epoch(model, data, optimizer):
"""
Run a train and validation epoch and return average bpd for each.
"""
traindata, valdata = data
model.train()
train_bpd = epoch_iter(model, traindata, optimizer)
model.eval()
val_bpd = epoch_iter(model, valdata, optimizer)
return train_bpd... | 5f441470347818e1c4f0fcdd67467100920bd6a0 | 35,563 |
def special_loss(logits, labels):
"""
This loss (and the rest of the training procedure) was taken from Philipp
Kraehenbuehl's code.
"""
mask = labels != 255
labels1 = tf.clip_by_value(labels, 0, 1)
lz = tf.nn.softplus(-tf.abs(logits)) * mask
return tf.reduce_sum(lz + (tf.to_float(logits... | 2dd1d3c967cf653a719ff993ff0b2de2d90404e2 | 35,564 |
def tobs():
"""Return a list of all tobs for the most active station as a list of JSON"""
# Query most active station
station_list = session.query(Measurement.station, func.count('*')).group_by(Measurement.station).order_by(func.count(Measurement.station).desc()).all()
mostactive=station_list[0][0]... | ad7461c3dacf715fee38a4fcdc292e58b2c48d2a | 35,565 |
from datetime import datetime
import sys
import torch
def _get_assignment_data_matches(net, mapping_assignment_dataloader, config,
sobel=False,
using_IR=False,
get_data_fn=None,
just_mat... | c130b2dde69cc58b6cbcd3777570fda8da0675e6 | 35,566 |
from scipy.special import lambertw
def prox_max_entropy(X, step, gamma=1, type="relative"):
"""Proximal operator for maximum entropy regularization.
g(x) = gamma sum_i x_i ln(x_i)
has the analytical solution of gamma W(1/gamma exp((X-gamma)/gamma)), where
W is the Lambert W function.
If type ==... | 7d5f1525ad1b7c413bad03b3aeba7b0af2e163ee | 35,567 |
def phase_vocode(audio_data: np.ndarray, speed: float) -> np.ndarray:
"""Applies phase vocoding to a 'np.ndarray' representing WAV data."""
reader = ArrayReader(audio_data.transpose())
writer = ArrayWriter(reader.channels)
phasevocoder(reader.channels, speed=speed).run(reader, writer)
return writer.... | e6d4d7e874c3f18c2c2a065b03d04d5e11d1963e | 35,568 |
import os
def fullPathListDir(dir: str) -> list:
"""
Return full path of files in provided directory
"""
return [os.path.join(dir, file) for file in os.listdir(dir)] | b456008e782e6f5a1d3471f5a9b5536ae4aad132 | 35,569 |
def partion_data_in_two(dataset, dataset_labels, in_sample_labels, oos_labels):
"""Partition dataset into in-distribution and OODs by labels.
Args:
dataset: the text from text_to_rank
dataset_labels: dataset labels
in_sample_labels: a list of newsgroups which the network will/did train on
oos_label... | df3eda7d64c9060c6a8f1d45dbf5a0d5cd3c2436 | 35,570 |
def check_and_update_generation_args(args):
"""
checks all generation commandline arguments. Since these arguments are all lists and shorthand can be used, we expand them to match the expected length
for instance, [1.0] becomes [1.0 1.0] if all other generation arguments are of length 2
"""
hyperpar... | 3d569b70b6ea4651af9cef0b7eafada1352b54a1 | 35,571 |
def category_condition_disable(request, structure_slug, category_slug,
condition_id, structure):
"""
Disables a condition from a category
:type structure_slug: String
:type category_slug: String
:type condition_id: Integer
:type structure: OrganizationalStructure ... | 87457c5b851bc791ec0e28d01100084948b9b58b | 35,572 |
def stitch_image_pair(img_a, img_b, stitch_direc):
"""Function to stitch image B to image A in the mentioned direction
Args:
img_a (numpy array): of shape (H, W, C) with opencv representation of image A (i.e C: B,G,R)
img_b (numpy array): of shape (H, W, C) with opencv representation of image B... | cc8143a3e9ebdae9a01c79a31a8fb7753bf0e2ee | 35,573 |
def as_composite(identifier: str) -> str:
"""
Translate the identifier of a mapry composite to a composite name in Python.
:param identifier: mapry identifier of a composite
:return: translated to a Python identifier of a composite
>>> as_composite(identifier='Some_URL_class')
'SomeURLClass'
... | 9e08c59acc60fbdb4ca4667f9d6b06502d521083 | 35,574 |
def find_saturation(freq, saturation_values, attenuation):
"""
Return a saturation value based on the frequency and amount of attenuation
:param int freq: the freq of interest, in Hz
:param saturation_values: a dict containing the saturation values (keys are frequencies)
:param attenuation: the amo... | a7f54ef3d80d0c1fbb5e51172812f2e4088dae1e | 35,575 |
def lstm_temporal(x, h0, Wx, Wh, b):
"""
Forward pass for an LSTM over an entire sequence of data. We assume an input
sequence composed of T vectors, each of dimension D. The LSTM uses a hidden
size of H, and we work over a minibatch containing N sequences. After running
the LSTM forward, we return ... | 04cd724d1fb7a996986b97d33b5a38ecefaf8185 | 35,576 |
from numpy.distutils.cpuinfo import cpu
import psutil
from typing import OrderedDict
import platform
def get_info_hardware():
"""Create a dictionary for CPU information."""
def _cpu_freq():
"""psutil can return `None` sometimes, esp. in Travis."""
func = "psutil.cpu_freq: "
try:
... | 33d6dc139218d1e45907bb58100cdc95300d8785 | 35,577 |
from pathlib import Path
def read_main_results_file():
"""Return a Series where each row is one of the COMSOL Main results"""
results_filepath = Path(MAIN_RESULTS_FILENAME)
results_series = pd.read_table(results_filepath,
sep=" ",
squ... | b5f66df57cd89763af2d95fb22039c49a71f22c5 | 35,578 |
def coveralls_enable(request):
"""Enable coveralls for an experiment"""
experiment = get_experiment_from_request_post(request)
travis_instance = experiment.travis
if travis_instance.enabled:
existing_config = enable_coveralls(travis_instance)
github_helper = get_github_helper(request, e... | df6021c2896eeaa8fcf395276d253023a69c5cba | 35,579 |
import time
from bs4 import BeautifulSoup
def download_book(book_id, title, thumbnail, rating_text):
"""
Download book id=`book_id` by calling the website's `getPage(.,.,.)` function.
"""
print('in download_book, book_id =', book_id)
with WebDriver("http://3asafeer.com/", delay=LOADING_WAIT_TIME_M... | f1ab4a91a1535fd25a5692a397222ff25f2216fe | 35,580 |
def games_per_time_period(df, days_per_period=7):
"""Return list of describing n matches played each time period in days, from start to end of dataframe"""
# define start and end dates to observe
start = df['date'].min()
# end is specified as 6 days after recorded final date of play, so pd.date_range be... | e0e327b8cdc8b04f2fde826cef90585e7e7be4cb | 35,581 |
def get_image_dims(image_data, check_is_rgb=False):
"""Decodes image and return its height and width.
Args:
image_data: Bytes data representing encoded image.
check_is_rgb: Whether to check encoded image is RGB.
Returns:
Decoded image size as a tuple of (height, width)
Raises:
ValueError: If ... | 745ff6dccc5c7ebb6052abc142e0b8a0ceda269a | 35,582 |
def open_mic_stream(pa, device_index, device_name):
""" Open microphone stream from first best microphone device. """
if not device_index and device_name:
device_index = find_input_device(device_name)
stream = pa.open(format=FORMAT, channels=CHANNELS, rate=RATE,
input=True, inp... | 8e69211e4aab87ca684a5ebf8ba222e2551f6734 | 35,583 |
def color_threshold(img):
"""
RGB color space threshold
:param img: Undistorted image
:return: Thresholded binary image
Ref: Course notes
"""
yellow = select_yellow(img)
white = select_white(img)
combined_binary = np.zeros_like(yellow)
combined_binary[(yellow >= 1) | (white >= 1)... | f11ddf7e452d7b8891562500819e41f9ea30bf0f | 35,584 |
def perturb_box(box, min_iou=0.5, sigma_factor=0.1, rng=None):
""" Perturb the input box by adding gaussian noise to the co-ordinates
args:
box - input box
min_iou - minimum IoU overlap between input box and the perturbed box
sigma_factor - amount of perturbation, relative to the box s... | 5ad15e766123f887e6cfc19b818efe4542e06148 | 35,585 |
def smootherstep(a, b, x):
"""Improved S-curve interpolation function.
Based on reference implementation of the improved algorithm proposed by
Ken Perlin that is available at https://en.wikipedia.org/wiki/Smoothstep
"""
x = clamp((x - a)/(b - a), 0.0, 1.0)
return x*x*x*(x*(x*6 - 15) + 10); | 6fa2e8694f2171f0e73aa19042aad2c69384a9e7 | 35,586 |
def _clean_conargs(**conargs):
"""Clean connection arguments"""
conargs['metadata'] = [x.strip() for x in conargs['metadata'].split(',') if x.strip()]
return conargs | f5942f750949ab674bd99778e79ea35c2d0bb775 | 35,587 |
import json
def select_customer():
"""Select customers from customer_name."""
cursor = mysql.cursor(MySQLdb.cursors.DictCursor)
TRN = request.form['TRN']
cursor.execute('''SELECT *
FROM Customer
WHERE TRN=%s''', (TRN,))
data = cursor.fetchone()
if da... | 8353a0d9bbcea731dd1ce0e2f031c22be5b673fe | 35,588 |
def is_date(string):
"""
Returns whether the string can be interpreted as a date from
using Python's dateutil.parser library. If it can parse, it will
return true, and false otherwise.
"""
try:
parse(string, fuzzy=False)
return True
except ValueError:
return False | d07ad17c8d3a24b28e21b42c0907e6e2c281f8d2 | 35,589 |
import argparse
import os
import logging
def get_adt_table(
args: argparse.Namespace,
edw: pyodbc.Connection,
query_directory: str,
) -> pd.DataFrame:
"""
Get ADT table through one of the following methods:
1. Provide ADT table
i. Filter patients by MRN
ii. Filter temporally
... | 895bfcaf21211a96ba6d8277918426576208eef1 | 35,590 |
def rosin_rammler(nbins, d50, md_total, sigma, rho_p, rho):
"""
This function is deprecated: Use psf.rosin_rammler() instead.
Return the volume size distribution from the Rosin Rammler distribution
Returns the fluid particle diameters in the selected number of bins on
a volume basis from ... | 3807c8c965caae492a3fecf6e803685cf7315710 | 35,591 |
def _get_layer(layer_idx, nn, for_pres):
""" Returns a tuple representing the layer label. """
if nn.layer_labels[layer_idx] in ['ip', 'op']:
fill_colour = _IPOP_FILLCOLOR
elif nn.layer_labels[layer_idx] in ['softmax', 'linear']:
fill_colour = _DECISION_FILLCOLOR
else:
fill_colour = _FILLCOLOR
lab... | 74ea378c5490eaf3c1e2cf7ab2413a55566725ea | 35,592 |
from resistics.sampling import to_timedelta
def inc_duration(win_size: int, olap_size: int, fs: float) -> RSTimeDelta:
"""
Get the increment between window start times
If the overlap size = 0, then the time increment between windows is simply
the window duration. However, when there is an overlap, th... | bdf754e3b1ace20cac1f99ef19dd04727594d710 | 35,593 |
def get_nearest(kd_node, point, dim, dist_func, return_distances=False, i=0, best=None):
"""
Find the closest neighbour of a point in a list of points using a KD-Tree.
Based on a recipe from code.activestate.com
"""
if kd_node:
dist = dist_func(point, kd_node[2])
dx = kd_node[2][i] -... | 480ac80404d16cb8ed4de9093a56326b15ad56b9 | 35,594 |
def plot_estimated_vs_simulated_edges(
graph,
sp_Graph,
lrn=None,
max_res_nodes=None,
lamb=1.0
):
"""Function to plot estimated vs simulated edge weights to look for significant deviations
"""
assert lamb >= 0.0, "lambda must be non-negative"
assert type(lamb) == float, "lambda must... | 7921715ccedaa192f291b228e9b12963ae8789dd | 35,595 |
def index_shape(geometry: Column, resolution: Column):
"""
Generate an H3 spatial index for an input GeoJSON geometry column.
This function accepts GeoJSON `Point`, `LineString`, `Polygon`, `MultiPoint`, `MultiLineString`, and `MultiPolygon`
input features, and returns the set of H3 cells at the specif... | a921f58eb31f24c3bbfb7b0b4e013b75ec2ad0f4 | 35,596 |
def mat_mul(
input_tensor, weight_tensor, activation=None, activation_params=None,
name="mat_mul"):
"""Compute a matrix multiplication for `input_tensor` and `weight_tensor`.
Args:
input_tensor: A 2D `Tensor`. Shaped as `NC`, where `N` is batch size and `C`
is number of channels.
weight_tenso... | f4b7755d6701438cd622837c976958dc511aa591 | 35,597 |
def get_events(wrapper, student: str = None, time: str = None) -> dict:
"""
list events
"""
start, end = get_dates(time)
event_data = wrapper.get_events(start_date=start,
end_date=end,
login=student)
return event_data | b682190334646889770c723693941da8c251db68 | 35,598 |
def merge_preclusters_ld(preclusters):
"""
Bundle together preclusters that satisfy the two criteria at the same time:
* 1. gwas_snp of clusterA is within ld_snps of clusterB (in LD)
* 2. (p-value of gwas_snp of clusterB * 10-3) <= p-value of gwas_snp of clusterA (<= p-value of gwas_snp of clusterB)
Args:
* ... | 64b0a82181df9afa352a796d4943b8392bb742d7 | 35,599 |
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